Taxonomic identification report

Sample ID: FungusB_Btub

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[analysis description + link to github repo]

Facility Hogwarts
Analyst John Doe
Analysis started 2025-05-03 01:28:15
Analysis completed 2025-05-03 01:28:15
Wall time 0:0:0 hours

Result overview

Inconclusive

Outcome: The analyst should attempt subjective species identification at the genus level.

Reasoning: [Flag 1C] >3 candidate species matched with high stringency (identity ≥ 98.5%).

Preliminary morphology ID confirmed? NA

Inconclusive taxonomic identity (Flag 1C) Fungi.

No taxa of interest provided at rank genus/species

Sample details

Locus ß-tub
Preliminary ID Fungi
Taxa of interest
Country Australia
Host Vitis vinifera
Sample ID FungusB_Btub
Query DNA sequence

Analyst evaluation

Identification of candidate species

Flag 1C: The analyst should attempt subjective species identification at the genus level
>3 candidate species matched with high stringency (identity ≥ 98.5%)

Candidate hits must meet ONE of these criteria:

Minimum alignment length 400bp
Minimum query coverage 85.0%

Candidate hits have then been classified as follows:

Classification Alignment identity Number of hits Number of species
STRONG MATCH ≥ 98.5% 216 7
MODERATE MATCH ≥ 93.5% NA NA
NO MATCH < 93.5%

Candidate species

Species Hits Identity E-value Database coverage
Neofusicoccum australe 91 100.0% 0.0
Neofusicoccum stellenboschiana 16 99.6% 0.0
Neofusicoccum cryptoaustrale 28 99.5% 0.0
Neofusicoccum luteum 72 99.5% 0.0
Neofusicoccum laricinum 2 99.1% 0.0
Neofusicoccum mangroviorum 6 99.0% 0.0
Neofusicoccum lumnitzerae 1 98.6% 0.0

Boxplot of BLAST hit identity percent grouped by genus

The boxplot above shows the distribution of BLAST hits identity within each genus. Each data point shows the alignment identity between the query sequence and reference sequence. The analyst may wish to refer to this figure when making a subjective genus-level identification for the sample.

Analyst evaluation

Taxa of interest (TOI)

This sections shows the taxa of interest (TOI) specified by the sample submitter. Each of these taxa has been cross-referenced against the candidate species to determine if they might match the taxonomic identity of the sample. A blank row indicates a TOI that did not match any candidate species, meaning that it is unlikely that the sample matches that TOI.

No Taxa of Interest to assess.

Reference sequence source diversity

This analysis evaluates how many independent sources have contributed to reference sequences for each candidate species. This provides a measure of confidence in the taxonomic annotation of references sequences. A sequence that has been annotated by multiple independent sources is more likely to have a correct taxonomic annotation.

Analyst evaluation

No candidate species to report on.

Intraspecies diversity

This section provides a phylogeny of the candidate reference sequences. The analyst can use this to make a subjective observation on how well the reference sequences are able to distinguish between species. If the phylogeny shows distinct clades for each species, we can be confident that the molecular data are capable of distinguishing between those species. However, if the phylogeny shows overlap between species, this reduces the capacity of the molecular data to confidently distinguish between those species. In some cases, we may see the query sequence falling outside of the adjacent species' clades, which indicates that our query species is not represented in the reference database, which could indicate a rare or novel species.

Analyst evaluation

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The phylogetic tree was constructed with FastME using the Neighbor-Joining method. Multiple-sequence alignment of the candidate reference sequences was performed using MAFFT. The visualization is rendered with TidyTree.

Taxonomy Check

The following resources can be used to ensure that the given taxonomy is legitimate and current.

Taxa Database
General GBIF
General ITIS
Mealybugs & scale ScaleNet database
Thrips Thripswiki
Spider Mites Spider Mites Database
Psocodea (Barklice, Booklice, and Parasitic Lice) Psocodea Species File Online
Orthoptera Orthoptera Species File Online
Drosophilidae TaxoDros
Diptera Catalog of the Diptera of the Australasian and Oceanian Regions
Systema Dipterorum
Aphids Aphid Species File
Ants AntWeb
AntCat
Lepidoptera (butterflies and moths) The Global Lepidoptera Names Index
Gracillariidae (primitive moths) Global Taxonomic Database of Gracillariidae
Pyralidae (pyralid moths) Global Information System on Pyraloidea
Tortricidae (tortrix moths) Tortricidae Resources on the Net